On the qq-Enumeration of Barely Set-Valued Tableaux and Plane Partitions

Barely set-valued tableaux are a variant of Young tableaux in which one box contains two numbers as its entry. It has recently been discovered that there are product formulas enumerating certain classes of barely set-valued tableaux. We give some q-analogs of these product formulas by introducing a version of major index for these tableaux. We also give product formulas and q-analogs for barely set-valued plane partitions. The proofs use several probability distributions on the set of order ideals of a poset, depending on the real parameter q > 0, which we think could be of independent interest.Comment: 38 pages, 6 tables, 3 figure

A Computational Framework for Solving Wasserstein Lagrangian Flows

The dynamical formulation of the optimal transport can be extended through various choices of the underlying geometry ($\textit{kinetic energy}$), and the regularization of density paths ($\textit{potential energy}$). These combinations yield different variational problems ($\textit{Lagrangians}$), encompassing many variations of the optimal transport problem such as the Schr\"odinger bridge, unbalanced optimal transport, and optimal transport with physical constraints, among others. In general, the optimal density path is unknown, and solving these variational problems can be computationally challenging. Leveraging the dual formulation of the Lagrangians, we propose a novel deep learning based framework approaching all of these problems from a unified perspective. Our method does not require simulating or backpropagating through the trajectories of the learned dynamics, and does not need access to optimal couplings. We showcase the versatility of the proposed framework by outperforming previous approaches for the single-cell trajectory inference, where incorporating prior knowledge into the dynamics is crucial for correct predictions

DynGFN: Towards Bayesian Inference of Gene Regulatory Networks with GFlowNets

One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes and their products that control gene expression and cellular function. We can treat this as a causal discovery problem but with two non-standard challenges: (1) regulatory networks are inherently cyclic so we should not model a GRN as a directed acyclic graph (DAG), and (2) observations have significant measurement noise, so for typical sample sizes there will always be a large equivalence class of graphs that are likely given the data, and we want methods that capture this uncertainty. Existing methods either focus on challenge (1), identifying cyclic structure from dynamics, or on challenge (2) learning complex Bayesian posteriors over DAGs, but not both. In this paper we leverage the fact that it is possible to estimate the "velocity" of gene expression with RNA velocity techniques to develop an approach that addresses both challenges. Because we have access to velocity information, we can treat the Bayesian structure learning problem as a problem of sparse identification of a dynamical system, capturing cyclic feedback loops through time. Since our objective is to model uncertainty over discrete structures, we leverage Generative Flow Networks (GFlowNets) to estimate the posterior distribution over the combinatorial space of possible sparse dependencies. Our results indicate that our method learns posteriors that better encapsulate the distributions of cyclic structures compared to counterpart state-of-the-art Bayesian structure learning approaches